MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : rhcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b2687 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b2799 b3945 b1602 b2913 b4381 b2406 b2868 b4064 b4464 b2366 b2492 b0904 b1533 b3821 b1380 b4141 b1798 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406257 (mmol/gDw/h)
  Minimum Production Rate : 0.309282 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.749208
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.244596
  EX_so4_e : 0.411586
  EX_pi_e : 0.391878
  EX_k_e : 0.079298
  EX_fe2_e : 0.006525
  EX_mg2_e : 0.003524
  EX_ca2_e : 0.002115
  EX_cl_e : 0.002115
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.212452
  EX_co2_e : 36.460937
  EX_h_e : 6.237275
  EX_ac_e : 1.265933
  EX_ade_e : 0.309555
  Auxiliary production reaction : 0.309282
  DM_5drib_c : 0.000273
  DM_4crsol_c : 0.000091

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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